pyproject.toml

[build-system]
build-backend = "setuptools.build_meta"
requires = ["setuptools>=62", "setuptools_scm[toml]>=8.0"]

[project]
name = "tlo"
authors = [
    {name = "Thanzi La Onse Model Development Team"},
]
classifiers = [
    'Development Status :: 3 - Alpha',
    'Intended Audience :: Science/Research',
    'License :: MIT',
    'Operating System :: OS Independent',
    'Programming Language :: Python :: 3',
    'Programming Language :: Python :: 3 :: Only',
    'Programming Language :: Python :: 3.11',
    'Programming Language :: Python :: 3.12',
]
dependencies = [
    "GitPython",
    "click",
    "matplotlib",
    "pyshp",
    "squarify",
    "numpy",
    "pandas~=2.0",
    "scipy",
     # Avoid https://foss.heptapod.net/openpyxl/openpyxl/-/issues/1963
    "openpyxl==3.1.0",
    # To submit jobs to Azure Batch
    "azure-batch",
    "azure-identity",
    "azure-keyvault",
    "azure-storage-file-share",
    # For saving and loading simulation state
    "dill",
]
description = "Thanzi la Onse Epidemiology Model"
dynamic = ["version"]
license = {file = "LICENSE.txt"}
readme = "README.md"
requires-python = ">=3.11"

[project.optional-dependencies]
dev = [
    # Running tests
    "pytest",
    "pytest-cov",
    "pytest-xdist",
    "virtualenv",
    "tox",
    # Linting
    "isort",
    "pylint",
    "ruff",
    # Profiling
    "ansi2html",
    "psutil",
    "pyinstrument>=4.3",
    # Building requirements files
    "pip-tools",
]

[project.scripts]
tlo = "tlo.cli:cli"

[project.urls]
repository = "https://github.com/UCL/TLOmodel"
documentation = "https://tlomodel.org"

[tool.coverage]
report = {show_missing = true, precision = 2}
run = {branch = true, parallel = true, source = [
    "tlo",
    "tests"
]}
paths.source = [
    "src",
    "*/site-packages",
]

[tool.isort]
force_single_line = false
multi_line_output = 3
include_trailing_comma = true
line_length = 100
known_first_party = "tlo"
default_section = "THIRDPARTY"
skip = ["src/tlo/_version.py"]

[tool.pylint.main]
extension-pkg-whitelist = ["numpy"]
disable = [
    "R",
    "C",
    "W",
    "E0606",  # possibly-used-before-assignment - gives a lot of false positives
]


[tool.pylint.typecheck]
signature-mutators = [
    "click.decorators.option",
    "click.decorators.argument",
    "click.decorators.version_option",
    "click.decorators.help_option",
    "click.decorators.pass_context",
    "click.decorators.confirmation_option",
]

[tool.pytest.ini_options]
testpaths = "tests"
python_files = [
    "test_*.py",
    "*_test.py",
    "tests.py",
]
addopts = "-ra --strict-markers --doctest-modules --doctest-glob=*.rst --tb=short"
markers = ["group2", "slow"]

[tool.ruff]
target-version = "py311"
line-length = 120

[tool.setuptools.packages.find]
where = ["src"]

[tool.setuptools_scm]
version_file  = "src/tlo/_version.py"
git_describe_command = ["git", "describe", "--dirty", "--tags", "--long", "--match", 'v[0-9]*']